Greg Von Kuster
18c95bb622
Improve logging for cleanup_datasets.py script.
2009-09-24 21:17:32 -04:00
Greg Von Kuster
947491b270
More improvement in cleanup_datasets script - will take significantly less disk, and may be faster.
2009-09-24 16:52:15 -04:00
Greg Von Kuster
a40bf886f1
Performance improvements in delete_datasets method in cleanup_datasets script ( hopefully enough ).
2009-09-24 12:21:41 -04:00
Ramkrishna Chakrabarty
299f8dd97f
Removed print stmts in listener
2009-09-21 15:40:58 -04:00
Ramkrishna Chakrabarty
50345092f4
added psycopg2 import stmt in galaxy_interface.py
2009-09-21 12:41:39 -04:00
Ramkrishna Chakrabarty
f99863cfd3
Galaxy AMQP messaging now uses amqp & sqlalchemy eggs
2009-09-21 12:06:33 -04:00
Ramkrishna Chakrabarty
c7d575208c
Fixed a bug in creating requests as an admin
2009-09-21 10:49:17 -04:00
Ramkrishna Chakrabarty
6b92bf6eb8
Galaxy AMQP Listener, first pass
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Added a check for testing completed requests in Requests functional tests
2009-09-18 15:18:57 -04:00
Nate Coraor
2abf463a95
More fixes for cleanup_datasets.py
2009-09-15 12:57:17 -04:00
Nate Coraor
f11dcd9781
Fix path mangling in cleanup_datasets.py
2009-09-14 12:23:16 -04:00
Greg Von Kuster
5665f1dbaf
Fix for cleanup_datasets.py script.
2009-09-11 11:26:26 -04:00
Daniel Blankenberg
52d1bc065a
Enable the cleanup_datasets script to purge Dataset Instances (HDAs, LDDAs) and mark base datasets as deleted without requiring the container (history, library/folder) to be deleted.
2009-08-10 11:53:28 -04:00
Daniel Blankenberg
460fd53bb7
Provide datatypes registry location when setting metadata externally.
2009-08-03 15:45:26 -04:00
Daniel Blankenberg
f4a7dbc436
Add a new flag -f/--force_retry to cleanup_datasets.py. This flag will cause the script to attempt to perform the requestion action on objects regardless if it has been performed before.
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This is useful, i.e. if purge_datasets was called with out using --remove_from_disk, but it is later decided to remove these files: the purge_datasets script should be called with both -r and -f.
2009-07-30 12:56:16 -04:00
Greg Von Kuster
0090622f59
Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features.
2009-06-05 11:15:25 -04:00
Nate Coraor
9113ceb29f
Fix the cleanup_datasets script
2009-05-28 15:18:49 -04:00
Nate Coraor
a6cc479643
Fix history deletion method in Galaxy check script
2009-05-05 13:03:23 -04:00
Daniel Blankenberg
da52bd848a
Add ability for admins to delete and undelete library items.
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Modify cleanup_datasets.py script and include a database migration script.
2009-04-23 12:42:05 -04:00
Nate Coraor
8b0dcb7e4d
Fixes for native Leopard Python eggs
2009-04-22 14:43:54 -04:00
Nate Coraor
f1304c73e6
Merged from central
2009-04-15 15:45:28 -04:00
Nate Coraor
187a2e25fa
Add database versioning support
2009-04-15 15:43:26 -04:00
James Taylor
adeef24ce9
Adding workflow tests using Selenium. These actually drive the web browser to test the Javascript UI effectively. Currently can't run under buildbot.
2009-03-27 18:55:00 -04:00
Greg Von Kuster
05c2d4222b
merging from central
2009-03-20 03:06:40 -04:00
Greg Von Kuster
354d0447df
Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.
2009-03-20 02:49:30 -04:00
Greg Von Kuster
da476a3f3a
merging from central
2009-03-17 23:57:08 -04:00
Greg Von Kuster
69e383d6a8
Integrating i18n support provided by Mitsuteru Nakao, Takashi Hatakeyama, and Hideyuki Morita.
2009-03-17 22:46:47 -04:00
Daniel Blankenberg
34a4a1f4d5
Fix for setting metadata externally when outputs_to_working_directory = True.
2009-03-06 12:32:31 -05:00
Daniel Blankenberg
50e385d4a5
Use JSON instead of pickle for setting metadata externally, except for DatasetInstance objects.
2009-03-05 12:53:57 -05:00
Daniel Blankenberg
df82f3e163
Add the ability for metadata to be set in an external process, this requires set_metadata_externally = True in universe_wsgi.ini.
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Currently this is supported in the local runner (long running set_meta() can now be canceled the same as with jobs) and in the non-staging PBS runner.
There is a slight change to how new Metadata FileParameters are to be created in datatype.set_meta(), see the MAF datatype.
TODO:
Prevent editing of metadata on a running job when metadata is to be set externally.
Have datasets which were copied before job completion use the metadata from the original output dataset; currently .set_meta() is called locally on these.
2009-03-03 12:54:06 -05:00
Daniel Blankenberg
dd8a3c6605
Make history.activatable_datasets return a list.
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Fix update_database_with_security_libraries.py script so that it works again.
2009-02-26 14:06:11 -05:00
James Taylor
cb592fa20b
Updating the packed versions of all javascripts.
2009-02-25 14:24:46 -05:00
Greg Von Kuster
19d61ff4cf
Make activatable_datasets a property of the History object, eliminating the problematic mapper.
2009-02-23 12:31:15 -05:00
Nate Coraor
bf606c99f8
merge
2009-01-30 11:39:39 -05:00
Nate Coraor
f8ce6fc19d
merge
2009-01-30 11:39:29 -05:00
Nate Coraor
dd2ba78f45
Add fetch_eggs option to pull for other platforms (e.g. cluster nodes)
2009-01-30 11:37:18 -05:00
Greg Von Kuster
cfde4c4015
Normalize the model supporting the new library features. This rev assumes all current Library tables will be dropped so they are re-created at server start-up ( all library data will be lost ). Normalized objects are as follows:
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1. ActionDatasetRoleAssociation -> DatasetPermissions ( renamed )
2. LibraryFolderDatasetAssociation -> LibraryDatasetDatasetAssociation ( renamed )
3. ActionLibraryItemRoleAssociation -> LibraryPermissions, LibraryFolderPermissions, LibraryDatasetPermissions, LibraryDatasetDatasetPermissions, LibraryItemInfoPermissions, LibraryItemInfoTemplatePermissions
4. LibraryItemInfoAssociation -> LibraryInfoAssociation, LibraryFolderInfoAssociation, LibraryDatasetInfoAssociation, LibraryDatasetDatasetInfoAssociation
5. LibraryItemInfoTemplateAssociation -> LibraryInfoTemplateAssociation, LibraryFolderInfoTemplateAssociation, LibraryDatasetInfoTemplateAssociation, LibraryDatasetDatasetInfoTemplateAssociation
2009-01-28 16:29:30 -05:00
Nate Coraor
5506ec8d3b
merging heads
2008-12-23 13:28:43 -05:00
Nate Coraor
80f42e4199
Since tempfiles seem to occasionally be left behind, allow logging of
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open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts. This
should be considered temporary and will be removed when it's determined
where/how this happens.
2008-12-23 13:28:27 -05:00
Nate Coraor
8fdd73aaed
merging heads
2008-12-23 13:28:24 -05:00
Greg Von Kuster
6a3f5a925e
Eagerload active_datasets for a history rather than activatable_datasets since it throws exceptions in the migration script.
2008-12-23 10:25:54 -05:00
Greg Von Kuster
61951c59e1
More optimization, code cleanup in migration script.
2008-12-23 09:29:58 -05:00
Greg Von Kuster
1cf912260d
Bug fixes for my last commit.
2008-12-22 17:12:20 -05:00
Greg Von Kuster
6d9db00839
Speed up script for migrating central to security.
2008-12-22 16:39:36 -05:00
Guruprasad Anada
0eb6e8d521
Pushing changes from central to security..
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G: Enter commit message. Lines beginning with 'HG:' are removed.
2008-12-22 13:38:00 -05:00
Guruprasad Anada
54dc919413
Script to enumerate GOPS JOIN jobs that could have returned an incorrect result before the issue with minimum overlap was fixed last week.
2008-12-22 13:35:01 -05:00
Guruprasad Anada
14e8c4fcad
speed enhancement for incorrect_gops_jobs script.
2008-12-17 12:13:38 -05:00
Guruprasad Anada
25cd5b63f5
central to security
2008-12-17 12:13:32 -05:00
Guruprasad Anada
6e266a9deb
Central to security
2008-12-17 11:26:32 -05:00
Guruprasad Anada
42263dd8b2
Fix for a minor bug in my previous commit.
2008-12-17 11:25:35 -05:00
Guruprasad Anada
8bd7ce669b
Commiting changes from central to security:
2008-12-17 11:03:27 -05:00
Greg Von Kuster